Uses of Package
de.jstacs.data.sequences.annotation

Packages that use de.jstacs.data.sequences.annotation
de.jstacs.data Provides classes for the representation of data. 
de.jstacs.data.sequences Provides classes for representing sequences. 
de.jstacs.data.sequences.annotation Provides the facilities to annotate Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class 
de.jstacs.io Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and Storables to an XML-representation 
de.jstacs.models.mixture.motif   
de.jstacs.motifDiscovery This package provides the framework including the interface for any de novo motif discoverer 
de.jstacs.scoringFunctions Provides ScoringFunctions that can be used in a ScoreClassifier
de.jstacs.scoringFunctions.mix Provides ScoringFunctions that are mixtures of other ScoringFunctions. 
de.jstacs.scoringFunctions.mix.motifSearch   
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.data
SequenceAnnotation
          Class for a general annotation of a Sequence.
SequenceAnnotationParser
          This interface declares the methods which are used by AbstractStringExtractor to annotate a String which will be parsed to a Sequence.
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.data.sequences
SequenceAnnotation
          Class for a general annotation of a Sequence.
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.data.sequences.annotation
LocatedSequenceAnnotation
          Class for a SequenceAnnotation that has a position on the sequence, e.g for transcription start sites or intron-exon junctions.
LocatedSequenceAnnotationWithLength
          Class for a SequenceAnnotation that has a position on the sequence and a length, e.g. for donor splice sites, exons or genes.
MotifAnnotation
          Class for a StrandedLocatedSequenceAnnotationWithLength that is a motif.
NullSequenceAnnotationParser
          This SequenceAnnotationParser returns always null as SequenceAnnotation.
SequenceAnnotation
          Class for a general annotation of a Sequence.
SequenceAnnotationParser
          This interface declares the methods which are used by AbstractStringExtractor to annotate a String which will be parsed to a Sequence.
SinglePositionSequenceAnnotation
          Class for some annotations that consist mainly of one position on a sequence.
SinglePositionSequenceAnnotation.Type
          This enum defines possible types of a SinglePositionSequenceAnnotation.
StrandedLocatedSequenceAnnotationWithLength
          Class for a SequenceAnnotation that has a position, a length and an orientation on the strand of a Sequence.
StrandedLocatedSequenceAnnotationWithLength.Strand
          This enum defines possible orientations on the strands.
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.io
SequenceAnnotation
          Class for a general annotation of a Sequence.
SequenceAnnotationParser
          This interface declares the methods which are used by AbstractStringExtractor to annotate a String which will be parsed to a Sequence.
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.models.mixture.motif
StrandedLocatedSequenceAnnotationWithLength.Strand
          This enum defines possible orientations on the strands.
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.motifDiscovery
MotifAnnotation
          Class for a StrandedLocatedSequenceAnnotationWithLength that is a motif.
StrandedLocatedSequenceAnnotationWithLength.Strand
          This enum defines possible orientations on the strands.
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.scoringFunctions
StrandedLocatedSequenceAnnotationWithLength.Strand
          This enum defines possible orientations on the strands.
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.scoringFunctions.mix
StrandedLocatedSequenceAnnotationWithLength.Strand
          This enum defines possible orientations on the strands.
 

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.scoringFunctions.mix.motifSearch
StrandedLocatedSequenceAnnotationWithLength.Strand
          This enum defines possible orientations on the strands.